A four-year-old North Atlantic right whale found dead in the Bay of Fundy had been hit by a ship, federal fisheries experts say.

A coast guard patrol found the 45-tonne, 14-metre whale floating off Yarmouth, in southwest Nova Scotia, on Sunday.

This is the second female right whale to be struck by a vessel in the Bay of Fundy this summer. A 25-tonne, nine-metre whale was found floating between the islands of Campobello and Grand Manan on July 24.

"It's certainly a big problem," said Jerry Conway, a marine mammal expert with the Department of Fisheries and Oceans. "We've lost a potential calf production, if you will, of about 20 animals."

The slow-moving North Atlantic right whale is an endangered species in Canada. There are only about 350 left, according to some estimates.

In recent years, marine scientists have managed to reroute shipping lanes in the Bay of Fundy to divert large tankers away from whale habitats.

But Conway said there's not much else that can be done to protect the whales, which are difficult to spot in fog or rough seas.

"They do spend a lot of time on the surface and have a very low profile on the surface, so mariners are aware [and] they do try to avoid them, but unfortunately these accidents do happen," he said.

Conway said the blubber from the whale found near Yarmouth will be buried, while the bones are going to the Museum of Natural History in Halifax.